Plans for tens of thousands of new houses, particularly for the south-east and East Anglia, may have to be redrawn or scrapped because of poor flood defences, the environment agency warned yesterday.

Government departments, local councils and the agency plan to meet over the next few weeks to reassess drainage schemes amid growing concern about the risk to areas earmarked for big developments. Expansion plans for Ashford in Kent, Milton Keynes, and Cambridgeshire, as well as a proposed Thames gateway "linear city" east of Dartford, are giving cause for concern.

The agency is also pressing for an urgent meeting with the Greater London authority to discuss improving the Thames barrier, which was considered an adequate safeguard until 2030; one senior official said improvements would probably be necessary well before then.

Immediate defence schemes will be needed to protect some of the 2m homes in England and Wales built on flood plains, invariably in the 70s and 80s when planning was relaxed. And, yesterday, the Association of British Insurers advised house buyers to employ surveyors to ask questions about flood risk before any exchange of contracts.

The ABI's director general, Mary Francis, said they were concerned about how the government would find sufficient suitable land for 3m new homes in England by 2016. The environment agency said many housing developments would have to be reconsidered or scrapped as too risky.

The agency also said it was concerned about pockets of housing going ahead against its advice. "We have worked hard at getting the message across to councils that they shouldn't allow developments in flood-risk areas," an official said. "Some have heeded our advice, but small schemes are slipping through and they gradually build up to present a much bigger problem."

Countryside groups also warned that developments would have to go back to the drawing board. Sarah Fowler, of the Royal Society for the Protection of Birds, said questions had to be raised about plans for up to 15,000 homes on the flatlands of Cambridgeshire. "This will produce more concrete and hard surfaces leading to massive water run-offs, raising the likelihood of more severe flooding."

The problems were compounded by the Ministry of Agriculture's encouragement of intensive farming which led to the drainage of wetlands in low-lying areas. "These flood-plain wetlands were a safety valve and we've replaced them with houses and under-drained farmland," Ms Fowler said. "So we have much higher flood peaks in a much shorter time-scale because there is nowhere to absorb the water."

Nevertheless, ministers are pressing ahead with plans for 43,000 new houses a year, in the south east, for the next 15 years. Serplan, the councils' planning consortium, wants that figure cut to 33,000 a year.

Sandy Bruce-Lockhart, leader of Kent county council, said his authority would ask the government to scale down housing projections. Kent is being told to take 129,000 houses by 2016 - 30% more than it wants.

The House Builders' Federation yesterday suggested councils should take some of the blame for construction in low-lying areas. "Developers can only put in planning applications, they cannot decide where houses are built," said its spokesman, Pierre Williams. "It is up to [councils] to assess the flood risk with the help of the environment agency."

Serplan put the blame partly on previous governments. Chris Williams, chair of Serplan's strategy group and Buckinghamshire's environmental services director, said Whitehall had been loath to let councils reject plans just on flood risk, so many questionable developments had been approved.